I can see where you were going with it now. I was going with "magical" in the sense that they didn't even try to put science behind it.

For example, jump gates, vaguely sciencey. Ship battles, spiced for television but with an eye for science.

Technomages, they say "science did it" in the same way you'd say "a wizard did it", so magical. This is intentional though, so I don't mind too much (even if I don't care for them).
Jason Ironheart transforming into energy, "science did it" level of magical.
Telepaths, "a vorlon did it".
The souls Soul Hunters collect depend on your interpretation. They're either sciencey imprints of a person or magical souls, but they definitely become magical whenever they escape and affect the real world in some scene I can vaguely remember.
The Minbari/human souls were intentionally vague so probably don't fit in the list.

Sheridan's end-game (along with Kosh) are also what I would qualify as magical, but I only generally remember what happened and not well enough to discuss.

...All of which is a long-winded way of saying, I see what you were talking about and have nothing of value to add. =]